Paramagnetism-based refinement strategy for the solution structure of human alpha-parvalbumin

Biochemistry. 2004 May 11;43(18):5562-73. doi: 10.1021/bi035879k.

Abstract

In the frame of a research aimed at the detailed structural characterization of human calcium-binding proteins of the EF-hand family, the solution structure of human alpha-parvalbumin has been solved by NMR and refined with the help of substitution of the Ca(2+) ion in the EF site with the paramagnetic Dy(3+) ion. A simple (1)H-(15)N HSQC spectrum allowed the NH assignments based on the properties of Dy(3+). This allowed us to exploit pseudocontact shifts and residual dipolar couplings for solution structure refinement. The backbone and heavy atom RMSD are 0.55 +/- 0.08 and 1.02 +/- 0.08 A, respectively, and decrease to 0.39 +/- 0.05 and 0.90 +/- 0.06 A upon refinement with paramagnetism-based restraints. The RMSD for the metal itself in the EF site in the refined structure is 0.26 +/- 0.12 A. Backbone NH R(1), R(2), and NOE measured at two temperatures show the protein to be relatively rigid. The NH orientations are well determined by the paramagnetism-based restraints. This allows us to detect small but significant local structural differences with the orthologue protein from rat, whose X-ray structure is available at 2.0 A resolution. All differences are related to local changes in the amino acidic composition.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amides / chemistry
  • Animals
  • Anisotropy
  • Calcium-Binding Proteins / chemistry*
  • Carbon Isotopes
  • Crystallography, X-Ray
  • Dysprosium / chemistry
  • EF Hand Motifs
  • Humans
  • Models, Molecular
  • Nitrogen Isotopes
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Parvalbumins / chemistry*
  • Protein Conformation
  • Protein Isoforms / chemistry
  • Protons
  • Rats
  • Solutions

Substances

  • Amides
  • Calcium-Binding Proteins
  • Carbon Isotopes
  • Nitrogen Isotopes
  • Parvalbumins
  • Protein Isoforms
  • Protons
  • Solutions
  • Dysprosium

Associated data

  • PDB/1RJV
  • PDB/1RK9